initial commit

run.sh

@@ -0,0 +1,53 @@
+#!/bin/bash -l
+
+#SBATCH --partition=normal
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=8
+#SBATCH --gres=gpu:1
+#SBATCH --exclude=linux-05,linux-08,linux-02,linux-03,linux-04,linux-07
+
+#if [ "$(gmx --version | grep "GROMACS version")" != GROMACS*2025.2* ] ; then
+#    echo "Version loaded is not 2025.2! Exiting!"
+#    exit 1
+#fi
+
+if [ -n "$SLURM_CPUS_PER_TASK" ]; then
+    NT="-nt $SLURM_CPUS_PER_TASK"
+elif [ $(nproc) -lt 9 ] ; then
+    NT="-nt $(nproc)"
+else
+    NT="-nt 8"
+fi
+
+WORKDIR="$(dirname $(readlink -f "$0"))"
+if [ "${WORKDIR%/*}" = "/var/lib/slurm/slurmd" ] ; then
+    WORKDIR="$(pwd)"
+fi
+
+mkdir -p "$WORKDIR/out"
+
+export GMX_MAXCONSTRWARN=-1;
+gmx -nobackup grompp \
+    -f $WORKDIR/mdp_parameters.mdp \
+    -o $WORKDIR/tpr_run.tpr \
+    -c $WORKDIR/gro_start.gro \
+    -r $WORKDIR/gro_start.gro \
+    -p $WORKDIR/topology.top \
+    -po $WORKDIR/out/mdp_mdout.mdp \
+    -maxwarn 6
+
+if [ $? != 0 ] ; then
+    echo "grompp failed, exiting"
+    exit 1
+fi
+
+gmx mdrun \
+    -s $WORKDIR/tpr_run.tpr \
+    -o $WORKDIR/out/trr_traj.trr \
+    -c $WORKDIR/out/out.gro \
+    -x $WORKDIR/out/xtc_traj.xtc \
+    -e $WORKDIR/out/edr_energy.edr \
+    -g $WORKDIR/out/log.log \
+    -cpo $WORKDIR/out/state.cpt \
+    -cpi $WORKDIR/out/state.cpt \
+    -cpt 1 -notunepme -v $NT